I completed my PhD in computational biology at Cold Spring Harbor Laboratory in the Watson School of Biological Sciences in 2017. Under my advisor, Mike Schatz, I worked primarily on cancer genomics, addressing the challenges inherent in studying complex genomes in order to detect and understand structural variations. I developed algorithms for utilizing the Pacific Biosciences long-read sequencing technologies to study cancer genomes including structural variations, gene fusions, and historically reconstructing oncogene copy-number amplifications.

Software

Assemblytics is a web application that calls variants from an assembly. It also does unique anchor filtering to remove bias from repetitive elements in the genome, and it produces several plots and summary tables as well as an interactive dot plot of all the alignments, marking which are unique and which are repetitive. Assemblytics is at assemblytics.com and the code is available on github as a command-line program or the whole web application

SplitThreader is an interactive cancer genome rearrangement analyzer including a graph computation component that calculates the distances between genes to evaluate the genomic evidence for gene fusions, and it is equally important as a visualization tool, enabling genomics researchers to get an overview of where major structural variations have taken place in the genome.

Ribbon: is an alignment visualizer specializing in complex variation and long reads, showing alignments to multiple chromosomes and how the alignments are placed along the read itself, a perspective important to long sequences that is completely left out by regular genome browsers. Ribbon is used by scientists to study complex variation, see alignments of long reads, evaluate the performance of assembly scaffolding algorithms, and understand how genomes of different species match up against each other.

Publications

“Assemblytics: a web analytics tool for the detection of variants from an assembly” is published in Bioinformatics, indexed on PubMed, and the preprint from the first version is on the BioRxiv